ArticlePloS one2014
AdaBoost based multi-instance transfer learning for predicting proteome-wide interactions between Salmonella and human proteins.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Article
- Investigating the Precise Identification of Citrullination Sites with High- Performance Score Metrics Using a Powerful Computation Predicting Tool.Combinatorial chemistry & high throughput screening · 2024Article
- 4acCPred: Weakly supervised prediction ofMolecular therapy. Nucleic acids · 2022Article
- Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data.Bioinformatics (Oxford, England) · 2021Article
- Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions.Frontiers in microbiology · 2021Review
- Structural proteomics, electron cryo-microscopy and structural modeling approaches in bacteria-human protein interactions.Medical microbiology and immunology · 2020Review
- A Bipartite Network Module-Based Project to Predict Pathogen-Host Association.Frontiers in genetics · 2019Article
- Review of computational methods for virus-host protein interaction prediction: a case study on novel Ebola-human interactions.Briefings in functional genomics · 2018Review
- Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis.BMC genomics · 2018Article
- Localized instance fusion of MRI data of Alzheimer's disease for classification based on instance transfer ensemble learning.Biomedical engineering online · 2018Article
- An improved approach to infer protein-protein interaction based on a hierarchical vector space model.BMC bioinformatics · 2018Article
- Multi-label ℓScientific reports · 2016Article
- Computational discovery of Epstein-Barr virus targeted human genes and signalling pathways.Scientific reports · 2016Article
- Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways.BMC bioinformatics · 2015Article
- A simple feature construction method for predicting upstream/downstream signal flow in human protein-protein interaction networks.Scientific reports · 2015Article
- A novel one-class SVM based negative data sampling method for reconstructing proteome-wide HTLV-human protein interaction networks.Scientific reports · 2015Article
- Article
- Computational approaches for prediction of pathogen-host protein-protein interactions.Frontiers in microbiology · 2015Review
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2 authors.
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Abstract
Pathogen-host protein-protein interaction (PPI) plays an important role in revealing the underlying pathogenesis of viruses and bacteria. The need of rapidly mapping proteome-wide pathogen-host interactome opens avenues for and imposes burdens on computational modeling. For Salmonella typhimurium, only 62 interactions with human proteins are reported to date, and the computational modeling based on such a small training data is prone to yield model overfitting. In this work, we propose a multi-instance transfer learning method to reconstruct the proteome-wide Salmonella-human PPI networks, wherein the training data is augmented by homolog knowledge transfer in the form of independent homolog instances. We use AdaBoost instance reweighting to counteract the noise from homolog instances, and deliberately design three experimental settings to validate the assumption that the homolog instances are effective to address the problems of data scarcity and data unavailability. The experimental results show that the proposed method outperforms the existing models and some predictions are validated by the findings from recent literature. Lastly, we conduct gene ontology based clustering analysis of the predicted networks to provide insights into the pathogenesis of Salmonella.
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